The Btau4.0 assembly was built using sequence from a Hereford cow and her sire [ 11].
For the 50S ribosome, the GREMLIN model was built using sequence data from ∼1500 non-redundant genomes; Figure 1D suggests that for complexes with such large numbers of aligned sequence, residue residue interactions across interfaces can be predicted with quite high confidence based on amino acid sequence covariation.
Moreover, when compared to the H1 phylogeny built using complete sequences from Europe [17], [19], [38], [39], it appears that the novel branches H1v, H1w and H1x identified during the course of this study are all African-specific.
Over the 439 473 out of 560 sodC nucleotides sequenced in these isolates, these meningococcal isolates were 99 100% identical to each other and 81% identical to an Hi sodC consensus that was built using two sequences from GenBank (accession numbers M84012 and AF549211).
The second one (MAPPER models) is specific to MAPPER, and was built using TFBS sequences from TRANSFAC that were not used in the TRANSFAC models.
This approach builds gene family trees using sequences from available completely sequenced genomes (currently, Arabidopsis, Oryza and Populus; Chlamydomonas reinhardtii is used as an outgroup in the gene tree analyses for orthology determination), such that all members of a given gene family are included.
The MT sequence protein profile was built using MT sequences obtained from NCBI database using psi-BLAST [ 55].
A pseudo-reference sequence (PRF) was built using the sequence reads from the parents and their segregating DH population.
(B ) 16S rRNA gene phylogeny built using one representative sequence from each order within Cyanobacteria from the Greengenes database (May 2011) (DeSantis et al., 2006 ) besides orders YS2, SM1D11, and mle1-12 from which all sequences were used.
It should be noted that this collection was built using traditional Sanger sequencing from poly A + RNA, which due to the low sensitivity of the method, contains mainly unequivocally transcribed genes.
